Nilearn

- API Allow passing arguments to [first_level_from_bids](https://nilearn.github.io/dev/modules/generated/nilearn.glm.first_level.first_level_from_bids.html#nilearn.glm.first_level.first_level_from_bids) to build first level models that include specific set of confounds by relying on the strategies from [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) ([4103](https://github.com/nilearn/nilearn/issues/4103) by [Rémi Gau](https://github.com/Remi-Gau)).

- Support passing t and F contrasts to [compute_contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.compute_contrast.html#nilearn.glm.compute_contrast) that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero ([4067](https://github.com/nilearn/nilearn/issues/4067) by [Rémi Gau](https://github.com/Remi-Gau)).

- [NiftiSpheresMasker](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiSpheresMasker.html#nilearn.maskers.NiftiSpheresMasker) now has generate_report method ([3102](https://github.com/nilearn/nilearn/issues/3102) by [Yasmin Mzayek](https://github.com/ymzayek) and [Nicolas Gensollen](https://nicolasgensollen.github.io/)).

- Update the CompCor strategy in [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) and [load_confounds_strategy](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy) to support fmriprep 21.x series and above. ([3285](https://github.com/nilearn/nilearn/issues/3285) by [Hao-Ting Wang](https://wanghaoting.com/)).

- Allow setting vmin in [plot_glass_brain](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_glass_brain.html#nilearn.plotting.plot_glass_brain) and [plot_stat_map](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_stat_map.html#nilearn.plotting.plot_stat_map) ([3993](https://github.com/nilearn/nilearn/issues/3993) by [Michelle Wang](https://github.com/michellewang)).

- When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar ([2833](https://github.com/nilearn/nilearn/#2833) by [Nicolas Gensollen](https://nicolasgensollen.github.io/)).

- Combine GLM examples plot_fixed_effect and plot_fiac_analysis into a a single example plot_two_runs_model ([3191](https://github.com/nilearn/nilearn/issues/3191) by [Taylor Salo](https://tsalo.github.io/) and [Rémi Gau](https://github.com/Remi-Gau)).

NEW

- The temp_file_lifetime parameter of interactive plots’ open_in_browser method is deprecated and has no effect ([4180](https://github.com/nilearn/nilearn/issues/4180) by [Jerome Dockes](https://jeromedockes.github.io/))..

Fixes

- [MultiNiftiMasker](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.MultiNiftiMasker.html#nilearn.maskers.MultiNiftiMasker) can now call [generate_report](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker.generate_report) which will generate a report for the first subject in the list of subjects ([4001](https://github.com/nilearn/nilearn/issues/4001) by [Yasmin Mzayek](https://github.com/ymzayek)).

- Make sure that all atlases and datasets fetchers return a description ([4215](https://github.com/nilearn/nilearn/issues/4215) [Rémi Gau](https://github.com/Remi-Gau)).

- Update the CompCor strategy in [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) and [load_confounds_strategy](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy) to support fmriprep 21.x series and above. ([3285](https://github.com/nilearn/nilearn/issues/3285) by [Hao-Ting Wang](https://wanghaoting.com/)).

- Fix [SimpleRegressionResults](https://nilearn.github.io/dev/modules/generated/nilearn.glm.SimpleRegressionResults.html#nilearn.glm.SimpleRegressionResults) to accommodate for the lack of a model attribute ([4071](https://github.com/nilearn/nilearn/issues/4071) [Rémi Gau](https://github.com/Remi-Gau))

- [clean_img](https://nilearn.github.io/dev/modules/generated/nilearn.image.clean_img.html#nilearn.image.clean_img) can now use kwargs clean__sample_mask argument to correctly reshape the nifti image to the dimensions of the mask in the output ([4051](https://github.com/nilearn/nilearn/issues/4051) by [Mia Zwally](https://github.com/MIZwally)).

- Fix plotting of an image with color bar when maximum value is exactly zero ([4204](https://github.com/nilearn/nilearn/issues/4204) by [Rémi Gau](https://github.com/Remi-Gau)).

- Code Fix PSC normalisation method applied by standardize_signal in [signal](https://nilearn.github.io/dev/modules/signal.html#module-nilearn.signal) ([4116](https://github.com/nilearn/nilearn/issues/4116) by [Hao-Ting Wang](https://wanghaoting.com/) and [Yasmin Mzayek](https://github.com/ymzayek)).

- Fixed inheritance of decoder classes to keep compatibility with scikit-learn>v1.3 ([4188](https://github.com/nilearn/nilearn/issues/4188) by [Yasmin Mzayek](https://github.com/ymzayek)).

- Make sure that all the fetchers for atlas and func from [nilearn.datasets](https://nilearn.github.io/dev/modules/datasets.html#module-nilearn.datasets) return a [sklearn.utils.Bunch](https://scikit-learn.org/stable/modules/generated/sklearn.utils.Bunch.html#sklearn.utils.Bunch). Add new behavior to [fetch_language_localizer_demo_dataset](https://nilearn.github.io/dev/modules/generated/nilearn.datasets.fetch_language_localizer_demo_dataset.html#nilearn.datasets.fetch_language_localizer_demo_dataset) to return output as Bunch. This behavior will become the default in version 0.13.0 ([4233](https://github.com/nilearn/nilearn/issues/4233) by [Rémi Gau](https://github.com/Remi-Gau)).

Enhancements

- [NiftiSpheresMasker](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiSpheresMasker.html#nilearn.maskers.NiftiSpheresMasker) now has generate_report method ([3102](https://github.com/nilearn/nilearn/issues/3102) by [Yasmin Mzayek](https://github.com/ymzayek) and [Nicolas Gensollen](https://nicolasgensollen.github.io/)).

- Allow passing Pandas Series of image filenames to [SecondLevelModel](https://nilearn.github.io/dev/modules/generated/nilearn.glm.second_level.SecondLevelModel.html#nilearn.glm.second_level.SecondLevelModel) ([4070](https://github.com/nilearn/nilearn/issues/4070) by [Rémi Gau](https://github.com/Remi-Gau)).

- Allow passing arguments to [first_level_from_bids](https://nilearn.github.io/dev/modules/generated/nilearn.glm.first_level.first_level_from_bids.html#nilearn.glm.first_level.first_level_from_bids) to build first level models that include specific set of confounds by relying on the strategies from [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) ([4103](https://github.com/nilearn/nilearn/issues/4103) by [Rémi Gau](https://github.com/Remi-Gau)).

- Support passing t and F contrasts to [compute_contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.compute_contrast.html#nilearn.glm.compute_contrast) that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero ([4067](https://github.com/nilearn/nilearn/issues/4067) by [Rémi Gau](https://github.com/Remi-Gau)).

- Multi-subject maskers’ generate_report method no longer fails with 5D data but instead shows report of first subject. User can index input list to show report for different subjects ([3935](https://github.com/nilearn/nilearn/issues/3935) by [Yasmin Mzayek](https://github.com/ymzayek)).

- Allow global_signal parameter in [load_confounds_strategy](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy) in denoise_strategy='compcor' ([4225](https://github.com/nilearn/nilearn/issues/4225) by [Hao-Ting Wang](https://wanghaoting.com/)).

- Add two_sided option for [binarize_img](https://nilearn.github.io/dev/modules/generated/nilearn.image.binarize_img.html#nilearn.image.binarize_img) ([4121](https://github.com/nilearn/nilearn/issues/4121) by [Steven Meisler](https://www.stevenmeisler.com/)).

- [generate_report](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiLabelsMasker.html#nilearn.maskers.NiftiLabelsMasker.generate_report) now uses appropriate cut coordinates when functional image is provided ([4099](https://github.com/nilearn/nilearn/issues/4099) by [Yasmin Mzayek](https://github.com/ymzayek) and [Nicolas Gensollen](https://nicolasgensollen.github.io/)).

- Mention the classification type (all-vs-one) in [Decoding of a dataset after GLM fit for signal extraction](https://nilearn.github.io/dev/auto_examples/02_decoding/plot_haxby_glm_decoding.html#sphx-glr-auto-examples-02-decoding-plot-haxby-glm-decoding-py) ([4122](https://github.com/nilearn/nilearn/issues/4122) by [Tamer Gezici](https://github.com/TamerGezici)).

- Add backslash to homogenize [Parcellations](https://nilearn.github.io/dev/modules/generated/nilearn.regions.Parcellations.html#nilearn.regions.Parcellations) documentation ([4042](https://github.com/nilearn/nilearn/issues/4042) by [Nikhil Krish](https://github.com/NIkhilgKrish)).

- Specify full form of LSS in [Beta-Series Modeling for Task-Based Functional Connectivity and Decoding](https://nilearn.github.io/dev/auto_examples/07_advanced/plot_beta_series.html#sphx-glr-auto-examples-07-advanced-plot-beta-series-py) ([4141](https://github.com/nilearn/nilearn/issues/4141) by [Tamer Gezici](https://github.com/TamerGezici)).

- Don’t fetch tmaps in examples if tmaps aren’t used in the example. ([4136](https://github.com/nilearn/nilearn/issues/4136) by [Christina Roßmanith](https://github.com/crossmanith)).

- Describe the return value in [fetch_abide_pcp](https://nilearn.github.io/dev/modules/generated/nilearn.datasets.fetch_abide_pcp.html#nilearn.datasets.fetch_abide_pcp) documentation ([4159](https://github.com/nilearn/nilearn/issues/4159) by [Suramya Pokharel](https://github.com/SuramyaP)).

- Allow setting vmin in [plot_glass_brain](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_glass_brain.html#nilearn.plotting.plot_glass_brain) and [plot_stat_map](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_stat_map.html#nilearn.plotting.plot_stat_map) ([3993](https://github.com/nilearn/nilearn/issues/3993) by [Michelle Wang](https://github.com/michellewang)).

- When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar ([2833](https://github.com/nilearn/nilearn/#2833) by [Nicolas Gensollen](https://nicolasgensollen.github.io/)).


Changes

- Expose scipy CubicSpline extrapolate parameter in [clean](https://nilearn.github.io/dev/modules/generated/nilearn.signal.clean.html#nilearn.signal.clean) to control the interpolation of censored volumes in both ends of the BOLD signal data ([4028](https://github.com/nilearn/nilearn/issues/4028) by [Jordi Huguet](https://github.com/jhuguetn)).

- Make nilearn.reporting._get_clusters_table module public and move copy_img out of nilearn._utils.niimg ([4166](https://github.com/nilearn/nilearn/issues/4166) by [Rémi Gau](https://github.com/Remi-Gau)).

- Private utility context manager write_tmp_imgs is refactored into function write_imgs_to_path ([4094](https://github.com/nilearn/nilearn/issues/4094) by [Yasmin Mzayek](https://github.com/ymzayek)).

- Move user facing function concat_niimgs out of private module nilearn._utils.niimg_conversions ([4167](https://github.com/nilearn/nilearn/issues/4167) by [Rémi Gau](https://github.com/Remi-Gau)).

- Remove leading underscore from non private functions to align with PEP8 ([4086](https://github.com/nilearn/nilearn/issues/4086) by [Rémi Gau](https://github.com/Remi-Gau)).

- Make decoding/proximal_operator explicitly private to align with PEP8 ([4153](https://github.com/nilearn/nilearn/issues/4153) by [Rémi Gau](https://github.com/Remi-Gau)).

- Make private functions public when used outside of their module nilearn.interface to align with PEP8 ([4168](https://github.com/nilearn/nilearn/issues/4168) by [Rémi Gau](https://github.com/Remi-Gau)).

- [img_to_signals_labels](https://nilearn.github.io/dev/modules/generated/nilearn.regions.img_to_signals_labels.html#nilearn.regions.img_to_signals_labels) will also return masked_atlas in release 0.15. Meanwhile, use return_masked_atlas parameter to enable/disable this behavior. ([3761](https://github.com/nilearn/nilearn/issues/3761) by [Mohammad Torabi](https://github.com/mtorabi59)).

- cation Rename the parameter contrast_type in [compute_contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.compute_contrast.html#nilearn.glm.compute_contrast) and attribute contrast_type in [Contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.Contrast.html#nilearn.glm.Contrast) to stat_type ([4191](https://github.com/nilearn/nilearn/issues/4191) by [Rémi Gau](https://github.com/Remi-Gau)).

- [plot_surf_roi](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_surf_roi.html#nilearn.plotting.plot_surf_roi) will raise a warning if roi_map contains negative or non-integer values; in version 0.13 this will be a ValueError ([4131](https://github.com/nilearn/nilearn/issues/4131) by [Michelle Wang](https://github.com/michellewang)).

- nilearn.datasets.fetch_bids_langloc_dataset will be deprecated in release 0.13 as it returns data simuilar to [fetch_language_localizer_demo_dataset](https://nilearn.github.io/dev/modules/generated/nilearn.datasets.fetch_language_localizer_demo_dataset.html#nilearn.datasets.fetch_language_localizer_demo_dataset) ([4219](https://github.com/nilearn/nilearn/issues/4219) by [Rémi Gau](https://github.com/Remi-Gau)).

- the default parameter of fd_threshold and std_dvars_threshold in [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) with be updated to match fmriprep default in version 0.13 ([4225](https://github.com/nilearn/nilearn/issues/4225) by [Hao-Ting Wang](https://wanghaoting.com/)).

- Combine GLM examples plot_fixed_effect and plot_fiac_analysis into a a single example plot_two_runs_model ([3191](https://github.com/nilearn/nilearn/issues/3191) by [Taylor Salo](https://tsalo.github.io/) and [Rémi Gau](https://github.com/Remi-Gau)).

- Switch to using tox to manage environments during development and testing. All plotting python dependencies (matplotlib AND plotly) are now installed when running pip install nilearn[plotting] ([4029](https://github.com/nilearn/nilearn/issues/4029) by [Rémi Gau](https://github.com/Remi-Gau)).

List of pull requests

* [MAINT] Post release 0.10.2 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4022
* [FIX] fix spelling by Remi-Gau in https://github.com/nilearn/nilearn/pull/4026
* [MAINT] Add python 3.12 to CI by Remi-Gau in https://github.com/nilearn/nilearn/pull/4023
* [FIX] Allow `MultiNiftiMasker` to use `generate_report` method by ymzayek in https://github.com/nilearn/nilearn/pull/4001
* [MAINT] Implement deprecation warnings-as-errors in prerelease test using pytest fixture by ymzayek in https://github.com/nilearn/nilearn/pull/3936
* [MAINT] Ignore private visual testing file when running pytest by ymzayek in https://github.com/nilearn/nilearn/pull/4030
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4041
* [DOC] Change all block splitters in examples to use short syntax by ymzayek in https://github.com/nilearn/nilearn/pull/4031
* [MAINT] Update issue labels by Remi-Gau in https://github.com/nilearn/nilearn/pull/4036
* [MAINT] Add partial build specific to CI doc build workflow by ymzayek in https://github.com/nilearn/nilearn/pull/4044
* [ENH] Allow setting `vmin` in `plot_glass_brain` and `plot_stat_map` by michellewang in https://github.com/nilearn/nilearn/pull/3993
* [MAINT] Use correct target name for Makefile recipe by ymzayek in https://github.com/nilearn/nilearn/pull/4045
* [MAINT] Rename and move testing utilities under tests directory in each module by ymzayek in https://github.com/nilearn/nilearn/pull/4047
* [MAINT] refactor is plotly installed by Remi-Gau in https://github.com/nilearn/nilearn/pull/4034
* [FIX] fix typos in Harvard Oxford atlas labels by Remi-Gau in https://github.com/nilearn/nilearn/pull/4035
* [ENH] add readme to default data locations by Remi-Gau in https://github.com/nilearn/nilearn/pull/4037
* [DOC] link terms to glossary by Remi-Gau in https://github.com/nilearn/nilearn/pull/4038
* [DOC] update URLs with `http://` to `https://` by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4050
* [DOC] Fix wrong indentation of example code by ymzayek in https://github.com/nilearn/nilearn/pull/4053
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4058
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4059
* [MAINT] Use rng fixture for setting up np.random.RandomState() - part 2 by ymzayek in https://github.com/nilearn/nilearn/pull/4054
* [MAINT] use affine_eye fixture by Remi-Gau in https://github.com/nilearn/nilearn/pull/4056
* [MAINT] Refactor fixture for plotting by Remi-Gau in https://github.com/nilearn/nilearn/pull/4057
* [DOC] move default from end of argument description to type name by Remi-Gau in https://github.com/nilearn/nilearn/pull/4040
* [MAINT fix typo in fixture name by Remi-Gau in https://github.com/nilearn/nilearn/pull/4062
* [MAINT] Pytest fixture to ignore internal deprecation warnings by ymzayek in https://github.com/nilearn/nilearn/pull/4043
* [MAINT] change function privacy in _utils by Remi-Gau in https://github.com/nilearn/nilearn/pull/4061
* [MAINT] change future warning to deprecation warning by Remi-Gau in https://github.com/nilearn/nilearn/pull/4060
* [MAINT] Use rng fixture for setting up `np.random.RandomState()` - part 1 by ymzayek in https://github.com/nilearn/nilearn/pull/4052
* [FIX] fix experimental example private function in monkeypatch by Remi-Gau in https://github.com/nilearn/nilearn/pull/4065
* [DOC] Formatting of docstring in regions.Parcellations by NIkhilgKrish in https://github.com/nilearn/nilearn/pull/4042
* [MAINT] Use rng fixture instead of check_random_state by Remi-Gau in https://github.com/nilearn/nilearn/pull/4063
* [STY] Minor doc formatting by Remi-Gau in https://github.com/nilearn/nilearn/pull/4072
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4075
* [ENH] Allow pandas.Series as valid input for second_level_input by Remi-Gau in https://github.com/nilearn/nilearn/pull/4070
* [ENH] pad t and F 'short' contrasts with zeros by Remi-Gau in https://github.com/nilearn/nilearn/pull/4067
* [DOC] Fix failing docs on main by ymzayek in https://github.com/nilearn/nilearn/pull/4079
* [MAINT] refactor of tests and code in GLM module by Remi-Gau in https://github.com/nilearn/nilearn/pull/4066
* [MAINT] drop python 3.7 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4033
* [DOC] Make scope limit more obvious regarding accepting new downloaders by Remi-Gau in https://github.com/nilearn/nilearn/pull/4080
* [DOC][MAINT] Remove restriction on Sphinx version by ymzayek in https://github.com/nilearn/nilearn/pull/4081
* [FIX] image.clean_img() kwargs integration by MIZwally in https://github.com/nilearn/nilearn/pull/4051
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4083
* [FIX] fix typo by Remi-Gau in https://github.com/nilearn/nilearn/pull/4091
* [MAINT] update DOI and add RRID by Remi-Gau in https://github.com/nilearn/nilearn/pull/4032
* [DOC] mention checking badges during release by Remi-Gau in https://github.com/nilearn/nilearn/pull/4085
* [MAINT] Fix Zenodo DOI badge by ymzayek in https://github.com/nilearn/nilearn/pull/4093
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4097
* [DOC] Remove extraneous hash symbols for examples' section splitters by ymzayek in https://github.com/nilearn/nilearn/pull/4096
* [DOC] Improve docstring rendering for typed experimental surface module by ymzayek in https://github.com/nilearn/nilearn/pull/4049
* [DOC] Add tagging of release version to stable doc build by ymzayek in https://github.com/nilearn/nilearn/pull/4100
* [FIX] Disable extrapolation of out-of-bounds volumes by jhuguetn in https://github.com/nilearn/nilearn/pull/4028
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4102
* [MAINT] Add listing utilities by NicolasGensollen in https://github.com/nilearn/nilearn/pull/2991
* [MAINT] Pin kaleido version to `0.1.0.post1` for windows by ymzayek in https://github.com/nilearn/nilearn/pull/4101
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4105
* [MAINT] Rewrite `write_tmp_imgs` function and use it with pytest's `tmp_path` by ymzayek in https://github.com/nilearn/nilearn/pull/4094
* [MAINT] Use Numpy Random Generator to replace legacy RandomState by ymzayek in https://github.com/nilearn/nilearn/pull/4084
* [MAINT] Store 1 timepoint for 4D generating a report with the maskers by ymzayek in https://github.com/nilearn/nilearn/pull/3935
* [DOC] Speed up fit computation with parallel processing by ymzayek in https://github.com/nilearn/nilearn/pull/4108
* [REF] Clarify code in `find_parcellation_cut_coords` function by ymzayek in https://github.com/nilearn/nilearn/pull/4107
* [MAINT] using tox to test in different environments by Remi-Gau in https://github.com/nilearn/nilearn/pull/4029
* [DOC] Fix label in changelog by Remi-Gau in https://github.com/nilearn/nilearn/pull/4114
* [DOC] Clarify docstrings of plotting functions in `img_plotting` by ymzayek in https://github.com/nilearn/nilearn/pull/4115
* [EHN] Implement signal.clean to SurfaceMasker by htwangtw in https://github.com/nilearn/nilearn/pull/4117
* [ENH] Update binarize_img for negative value handling by smeisler in https://github.com/nilearn/nilearn/pull/4121
* [ENH] Colorbar ticks at threshold values by NicolasGensollen in https://github.com/nilearn/nilearn/pull/2887
* [ENH] Add new returns to `NiftiLabelsMasker`'s `transform` output by mtorabi59 in https://github.com/nilearn/nilearn/pull/3761
* [ENH] Set appropriate cut coordinates for NiftiLabelsMasker reports by ymzayek in https://github.com/nilearn/nilearn/pull/4099
* [MAINT] minor pre-commit fix by Remi-Gau in https://github.com/nilearn/nilearn/pull/4125
* [ENH] Let _check_embedded_nifti_masker work with surface masker by ymzayek in https://github.com/nilearn/nilearn/pull/4120
* [MAINT] Test against Numpy 2.0 nightly releases by ymzayek in https://github.com/nilearn/nilearn/pull/4130
* [MAINT] Remove trigger on PR for numpy2 test by ymzayek in https://github.com/nilearn/nilearn/pull/4133
* [DOC] Mention classification type in plot_haxby_glm_decoding.py by TamerGezici in https://github.com/nilearn/nilearn/pull/4122
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4134
* [MAINT] remove leading underscore from non private functions by Remi-Gau in https://github.com/nilearn/nilearn/pull/4086
* [ENH] `NiftiSpheresMasker` reports by NicolasGensollen in https://github.com/nilearn/nilearn/pull/3102
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4142
* Bump actions/setup-python from 4 to 5 by dependabot in https://github.com/nilearn/nilearn/pull/4143
* Don't use get_tmaps=True if tmaps aren't used by crossmanith in https://github.com/nilearn/nilearn/pull/4136
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4148
* [ENH] Raise error when negative or non-integer ROI values are passed to `plot_surf_roi` by michellewang in https://github.com/nilearn/nilearn/pull/4131
* [DOC] Specify full form of LSS in beta series tutorial by TamerGezici in https://github.com/nilearn/nilearn/pull/4141
* [MAINT] Apply Black to nifti_labels_masker.py by ymzayek in https://github.com/nilearn/nilearn/pull/4146
* [MAINT] Apply Black to reporting files by ymzayek in https://github.com/nilearn/nilearn/pull/4145
* [MAINT] Apply Black img_plotting.py by ymzayek in https://github.com/nilearn/nilearn/pull/4147
* [INFRA] Remove CI workflow to error on DeprecationWarnings of dependencies by ymzayek in https://github.com/nilearn/nilearn/pull/4149
* [MAINT] Apply Black to nifti_spheres_masker.py by ymzayek in https://github.com/nilearn/nilearn/pull/4144
* [MAINT] Improve error for nifti masker when fit is called without imgs or mask_img by ymzayek in https://github.com/nilearn/nilearn/pull/4151
* [MAINT] make proximal_operator a private module by Remi-Gau in https://github.com/nilearn/nilearn/pull/4153
* [ENH] rename `nilearn.datasets._utils.fetch_file` to `nilearn.datasets._utils.fetch_single_file` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4156
* [MAINT] make `__all__` and API doc more consistent by Remi-Gau in https://github.com/nilearn/nilearn/pull/4157
* [MAINT] relocate functions from nilearn.datasets.utils by Remi-Gau in https://github.com/nilearn/nilearn/pull/4154
* [FIX] Load compcor related confounds generated from fmriprep 21.x series by htwangtw in https://github.com/nilearn/nilearn/pull/3285
* [STY] run black on nilearn/interfaces/fmriprep by Remi-Gau in https://github.com/nilearn/nilearn/pull/4163
* [FIX] Adjust figure size to display title for functions calling `plot_surf` by ymzayek in https://github.com/nilearn/nilearn/pull/4164
* [FIX] fix SimpleRegressionResults by Remi-Gau in https://github.com/nilearn/nilearn/pull/4071
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4169
* [ENH] integrate load_confounds into first_level_from_bids by Remi-Gau in https://github.com/nilearn/nilearn/pull/4103
* Bump actions/upload-artifact from 3 to 4 by dependabot in https://github.com/nilearn/nilearn/pull/4170
* Updated docs for fetch_abide_pcp by SuramyaP in https://github.com/nilearn/nilearn/pull/4159
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4174
* [MAINT] nilearn.interface: make private functions used outside of their module public by Remi-Gau in https://github.com/nilearn/nilearn/pull/4168
* [DOC] link surface terms to glossary by Remi-Gau in https://github.com/nilearn/nilearn/pull/4161
* [STY] apply black to `nilearn._utils.data_gen` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4171
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4179
* [INFRA] Proposal for building stable docs in remote runner for releases by ymzayek in https://github.com/nilearn/nilearn/pull/4160
* [INFRA] Quick fix for automated stable doc build by ymzayek in https://github.com/nilearn/nilearn/pull/4181
* [INFRA] Fix auto trigger for release doc build in Actions workflow by ymzayek in https://github.com/nilearn/nilearn/pull/4182
* [FIX] use a local server rather than temp file to open plots in a browser by jeromedockes in https://github.com/nilearn/nilearn/pull/4180
* [FIX] rich display in jupyter notebook/lab by jeromedockes in https://github.com/nilearn/nilearn/pull/4183
* [MAINT] move user facing functions out of private modules by Remi-Gau in https://github.com/nilearn/nilearn/pull/4166
* [MAINT] move user facing functions out of private modules - part 2 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4167
* [FIX] use parameter deprecation decorator by Remi-Gau in https://github.com/nilearn/nilearn/pull/4189
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4193
* [STY] deal with private functions in nilearn.glm that do not coform to PEP8 naming by Remi-Gau in https://github.com/nilearn/nilearn/pull/4190
* [ENH] Allow string expressions for `second_level_contrast` of `non_parametric_inference` by ymzayek in https://github.com/nilearn/nilearn/pull/4150
* [FIX] rename `contrast_type` to `stat_type` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4191
* [DOC] fix edit button for examples by Remi-Gau in https://github.com/nilearn/nilearn/pull/4196
* [MAINT] remove duplicate dependency by Remi-Gau in https://github.com/nilearn/nilearn/pull/4199
* [MAINT] remove some old mention of nistats by Remi-Gau in https://github.com/nilearn/nilearn/pull/4200
* [MAINT] make private functions in `nilearn.plotting` used outside of their module public by Remi-Gau in https://github.com/nilearn/nilearn/pull/4197
* [MAINT] testing minimal version of dependencies by Remi-Gau in https://github.com/nilearn/nilearn/pull/4068
* [MAINT] sort changelog by labels by Remi-Gau in https://github.com/nilearn/nilearn/pull/4201
* [MAINT] Remove unnecessary lines describe in `test_clean_psc` by paul-reiners in https://github.com/nilearn/nilearn/pull/4208
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4213
* [DOC] format citation by Remi-Gau in https://github.com/nilearn/nilearn/pull/4212
* [DOC] replace `session` by `run` to align with BIDS terminology by Remi-Gau in https://github.com/nilearn/nilearn/pull/4214
* Bump actions/setup-python from 4 to 5 by dependabot in https://github.com/nilearn/nilearn/pull/4217
* [FIX] fix plotting of an image with color bar when maximum value is exactly zero by Remi-Gau in https://github.com/nilearn/nilearn/pull/4204
* [FIX] Fix PSC normalization when a high-pass filter is applied by ymzayek in https://github.com/nilearn/nilearn/pull/4116
* [MAINT] Adapt decoder for scikit-learn > 1.3 by ymzayek in https://github.com/nilearn/nilearn/pull/4188
* [DOC] update dataset descriptions by Remi-Gau in https://github.com/nilearn/nilearn/pull/4215
* [DOC] Combine similar two-runs GLM examples by tsalo in https://github.com/nilearn/nilearn/pull/3191
* [MAINT] speed up tests for html reports by Remi-Gau in https://github.com/nilearn/nilearn/pull/4221
* [DEP] deprecate bids_langloc fetcher by Remi-Gau in https://github.com/nilearn/nilearn/pull/4219
* FIX/EHN update load_confound_strategy defaults by htwangtw in https://github.com/nilearn/nilearn/pull/4225
* [FIX] Let decoder accept list of paths as input by ymzayek in https://github.com/nilearn/nilearn/pull/4227
* [FIX] Ensure that fetchers for atlas and func return a Bunch by Remi-Gau in https://github.com/nilearn/nilearn/pull/4233
* [MAINT] Examples output all their results in a single main directory by Remi-Gau in https://github.com/nilearn/nilearn/pull/4230
* Bump actions/cache from 3 to 4 by dependabot in https://github.com/nilearn/nilearn/pull/4234
* [DOC] update version in sphinx directives by Remi-Gau in https://github.com/nilearn/nilearn/pull/4238
* [DOC] sort changelog and add highlights by Remi-Gau in https://github.com/nilearn/nilearn/pull/4237
* [STY] apply black 24.1.0 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4162
* [DOC] remove warning from experimental module and add it as doc string by Remi-Gau in https://github.com/nilearn/nilearn/pull/4240
* [STY] re apply black by Remi-Gau in https://github.com/nilearn/nilearn/pull/4241

**Released November 2024**

List of pull requests

* [MAINT] Post release 0.10.4 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4366
* [MAINT] clean up makefiles and allow color in CLI in github workflows by Remi-Gau in https://github.com/nilearn/nilearn/pull/4370
* [DOC] update release procotol by Remi-Gau in https://github.com/nilearn/nilearn/pull/4371
* Change "resting state" to "movie watching" in compare means example by man-shu in https://github.com/nilearn/nilearn/pull/4373
* [DOC] Mention in style guide the meaning of trailing underscore for attributes by Remi-Gau in https://github.com/nilearn/nilearn/pull/4374
* [REF] Refactor CSS and html masker reports by Remi-Gau in https://github.com/nilearn/nilearn/pull/4372
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4381
* [FIX] skip problematic plotting in doc build by Remi-Gau in https://github.com/nilearn/nilearn/pull/4383
* [ENH] enhance `save_glm_to_bids` outputs by Remi-Gau in https://github.com/nilearn/nilearn/pull/4375
* [MAINT] change schedule of GH workflows by Remi-Gau in https://github.com/nilearn/nilearn/pull/4386
* [MAINT] monitor duration of doc build by Remi-Gau in https://github.com/nilearn/nilearn/pull/4387
* [MAINT] pre-download data on full doc build by Remi-Gau in https://github.com/nilearn/nilearn/pull/4390
* [FIX] fix flake8 bugbear errors by Remi-Gau in https://github.com/nilearn/nilearn/pull/4384
* [MAINT] improve workflow to test on nightly dependencies by Remi-Gau in https://github.com/nilearn/nilearn/pull/4364
* [MAINT] update precommit configuration by Remi-Gau in https://github.com/nilearn/nilearn/pull/4391
* [MAINT] update parameters for `scipy.sparse.linalg.cg` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4394
* [FIX] remove, implement or better document "unused" arguments by Remi-Gau in https://github.com/nilearn/nilearn/pull/4273
* [MAINT] Update circle-ci trigger-hosting by Remi-Gau in https://github.com/nilearn/nilearn/pull/4402
* [REF] refactor style checks in CI by Remi-Gau in https://github.com/nilearn/nilearn/pull/4406
* [MAINT] test on several macos versions by Remi-Gau in https://github.com/nilearn/nilearn/pull/4405
* [DOC] Fix typos found by codespell by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4410
* FIX failing `load_confound` test related to standardisation by htwangtw in https://github.com/nilearn/nilearn/pull/4411
* add width input to view_img() by alexsayal in https://github.com/nilearn/nilearn/pull/4416
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4418
* [FIX] Raise error if unknown kwargs are given to `first_level_from_bids` by michellewang in https://github.com/nilearn/nilearn/pull/4414
* [FIX] Refactor design matrix and contrast formula for the two-sample T-test example by YCHuang0610 in https://github.com/nilearn/nilearn/pull/4407
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4422
* [MAINT] only on use macOS-latest by Remi-Gau in https://github.com/nilearn/nilearn/pull/4424
* [MAINT] pacify codepspell by Remi-Gau in https://github.com/nilearn/nilearn/pull/4430
* [ENH] add plotting functions to the experimental surface module by jeromedockes in https://github.com/nilearn/nilearn/pull/4235
* [ENH] Adapt FirstLevelModel to work with surface data objects from new API by ymzayek in https://github.com/nilearn/nilearn/pull/4126
* Copy input image header to the output by default by man-shu in https://github.com/nilearn/nilearn/pull/4397
* Example to demonstrate `copy_header_from` in `math_img` by man-shu in https://github.com/nilearn/nilearn/pull/4392
* [STY] apply black to files no longer invovled in other pull requests by Remi-Gau in https://github.com/nilearn/nilearn/pull/4433
* [ENH] Add warning for future change of the default of `force_resample` to True by ajoshiusc in https://github.com/nilearn/nilearn/pull/4412
* [MAINT] remove some try/except on imports by Remi-Gau in https://github.com/nilearn/nilearn/pull/4440
* [ENH] add footer to all masker reports by Remi-Gau in https://github.com/nilearn/nilearn/pull/4307
* [ENH] expand surface plotting with new surface object by Remi-Gau in https://github.com/nilearn/nilearn/pull/4431
* [ENH] update example to show parametric modulation by Remi-Gau in https://github.com/nilearn/nilearn/pull/4436
* [MAINT] add force_resample where missing by Remi-Gau in https://github.com/nilearn/nilearn/pull/4441
* [DOC] add ...CV in logistic estimator name by man-shu in https://github.com/nilearn/nilearn/pull/4438
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4447
* [REF] add force_resample default to cached calls by Remi-Gau in https://github.com/nilearn/nilearn/pull/4450
* [ENH] add report for SurfaceMasker by Remi-Gau in https://github.com/nilearn/nilearn/pull/4432
* [MAINT] remove duplicate code by Remi-Gau in https://github.com/nilearn/nilearn/pull/4449
* [DOC] Fix deploy doc on main by Remi-Gau in https://github.com/nilearn/nilearn/pull/4455
* [REF] minor refactor of get_cmap and matplotlib version-handling by Remi-Gau in https://github.com/nilearn/nilearn/pull/4458
* [REF] refactor report templates by Remi-Gau in https://github.com/nilearn/nilearn/pull/4460
* [FIX] throw warning a masker `generate_report` is called without matplotlib by Remi-Gau in https://github.com/nilearn/nilearn/pull/4457
* [FIX] use string as label names in example involving the new surface based destrieux atlas by Remi-Gau in https://github.com/nilearn/nilearn/pull/4462
* [REF] refactor FLM fitting by Remi-Gau in https://github.com/nilearn/nilearn/pull/4461
* [MAINT] for monitoring of duration of CI only plot doc build on main (full builds) by Remi-Gau in https://github.com/nilearn/nilearn/pull/4463
* [MAINT] rename `tr` variable - private occurences by Remi-Gau in https://github.com/nilearn/nilearn/pull/4468
* [ENH] Replace `tr` by `t_r` in HRF generating functions and examples by Remi-Gau in https://github.com/nilearn/nilearn/pull/4470
* [FIX] pacify ruff warning about numpy 2 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4477
* [FIX] coerce loaded data from NKI to float in examples by Remi-Gau in https://github.com/nilearn/nilearn/pull/4475
* [ENH] add function to plot regressor correlation matrix by Remi-Gau in https://github.com/nilearn/nilearn/pull/4467
* [ENH] use nilearn `logger.log` function instead of `print` or `sys.stderr.write` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4469
* [FIX] change creation of region_names and add test by mtorabi59 in https://github.com/nilearn/nilearn/pull/4360
* [FIX] fix trigger hosting of doc of PR on circle-ci by Remi-Gau in https://github.com/nilearn/nilearn/pull/4481
* [FIX] Change default `ratio` value in glover to fit canonical Glover HRF (1999) by const7 in https://github.com/nilearn/nilearn/pull/4452
* Update second_level.py by arovai in https://github.com/nilearn/nilearn/pull/4483
* [MAINT] use pytest-reporter-html1 to create test reports by Remi-Gau in https://github.com/nilearn/nilearn/pull/4444
* Revert "[MAINT] use pytest-reporter-html1 to create test reports" by Remi-Gau in https://github.com/nilearn/nilearn/pull/4485
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4487
* [FIX] host doc from PR on Circle-CI by Remi-Gau in https://github.com/nilearn/nilearn/pull/4494
* Explain Decoder's default cross-validation scheme by man-shu in https://github.com/nilearn/nilearn/pull/4491
* Change default `clustering_percentile` in `_BaseDecoder` docstring by man-shu in https://github.com/nilearn/nilearn/pull/4489
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4499
* [DOC] Small correction on instructions for setting up environment by kimsin98 in https://github.com/nilearn/nilearn/pull/4459
* [API] renamed `ax` parameter for consistency by muddi900 in https://github.com/nilearn/nilearn/pull/4476
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4504
* [FIX] Reduce `dtype` of mask from `int64` to `int8` in `image.binarize_img` by psadil in https://github.com/nilearn/nilearn/pull/4502
* [FIX] force np.float64 format for second level matrix dataframe by Remi-Gau in https://github.com/nilearn/nilearn/pull/4503
* [MAINT] Finish adding tests for `_utils.data_gen` by kimsin98 in https://github.com/nilearn/nilearn/pull/4465
* [REF] refactor nibabel import by Remi-Gau in https://github.com/nilearn/nilearn/pull/4506
* [ENH] improve I/O for SurfaceImage by Remi-Gau in https://github.com/nilearn/nilearn/pull/4446
* [FIX] revert save analyze for SPM auditory data by Remi-Gau in https://github.com/nilearn/nilearn/pull/4508
* [MAINT] use pytest-reporter-html1 to create test reports by Remi-Gau in https://github.com/nilearn/nilearn/pull/4486
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4514
* [ENH] Change Butterworth filtering in nilearn.signal.clean to use 'sos' output by Remi-Gau in https://github.com/nilearn/nilearn/pull/4510
* [STY] apply black to remaining example by Remi-Gau in https://github.com/nilearn/nilearn/pull/4518
* [STY] apply black to remaining files in plotting subpackage by Remi-Gau in https://github.com/nilearn/nilearn/pull/4520
* [STY] apply black to surface subpackage by Remi-Gau in https://github.com/nilearn/nilearn/pull/4519
* [REF] remove obsolete try import by Remi-Gau in https://github.com/nilearn/nilearn/pull/4528
* [MAINT] Handle 2 numpy and matplolib deprecation warnings by Remi-Gau in https://github.com/nilearn/nilearn/pull/4522
* [MAINT] raise stacklevel of `copy_header` warning by Remi-Gau in https://github.com/nilearn/nilearn/pull/4530
* [MAINT] remove flynt config by Remi-Gau in https://github.com/nilearn/nilearn/pull/4532
* [MAINT] Clean up some warnings from the tests by Remi-Gau in https://github.com/nilearn/nilearn/pull/4529
* [FIX] return 3D effect maps for t contrasts by Remi-Gau in https://github.com/nilearn/nilearn/pull/4439
* Bump peter-evans/create-pull-request from 6 to 7 by dependabot in https://github.com/nilearn/nilearn/pull/4537
* [MAINT] reduce occurence of resampling related warnings by Remi-Gau in https://github.com/nilearn/nilearn/pull/4531
* [MAINT] simplify dependencies of `dev` and `style` installs by Remi-Gau in https://github.com/nilearn/nilearn/pull/4541
* [FIX] update scikit-learn decoder tags by Remi-Gau in https://github.com/nilearn/nilearn/pull/4535
* [FIX] remove several typos or double space by Remi-Gau in https://github.com/nilearn/nilearn/pull/4545
* [FIX] fix version to check for scikit learn for new decoder tags by Remi-Gau in https://github.com/nilearn/nilearn/pull/4546
* [MAINT] replace `nb` by `n` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4548
* [FIX] fix sklearn version check by Remi-Gau in https://github.com/nilearn/nilearn/pull/4550
* [REF] refactor nifti maskers tests by Remi-Gau in https://github.com/nilearn/nilearn/pull/4388
* [ENH] add optional pretty printing with rich for logging by Remi-Gau in https://github.com/nilearn/nilearn/pull/4544
* [FIX] only use tight_layout when figure is owned by larsoner in https://github.com/nilearn/nilearn/pull/4542
* [ENH] Add last version of the AAL atlas to its fetcher by JLefortBesnard in https://github.com/nilearn/nilearn/pull/4554
* [FIX] fix radiological view by Remi-Gau in https://github.com/nilearn/nilearn/pull/4556
* [FIX] fix name of parameter in the "extract_type" definition by Remi-Gau in https://github.com/nilearn/nilearn/pull/4559
* [FIX] `load_confounds`: Raise an exception when all volumes are scrubbed by victoris93 in https://github.com/nilearn/nilearn/pull/4558
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4564
* [MAINT] Optimize `_resample_one_img` logic check for nearest interpolation by kaitj in https://github.com/nilearn/nilearn/pull/4571
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4572
* [FIX] avoid warning when creating int64 images by Remi-Gau in https://github.com/nilearn/nilearn/pull/4555
* [MAINT] drop python 3.8 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4516
* [STY] Start using and configuring ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4574
* [STY] run ruff on extra files excluded from previous PR by Remi-Gau in https://github.com/nilearn/nilearn/pull/4578
* [DOC] add youtube channel in the doc footer by Remi-Gau in https://github.com/nilearn/nilearn/pull/4580
* [FIX] `first_level_from_bids` will now return subjects in order by tharun634 in https://github.com/nilearn/nilearn/pull/4582
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4584
* [ENH] use BIDS version of the SPM auditory dataset by Remi-Gau in https://github.com/nilearn/nilearn/pull/4515
* [STY] fix error D209 from ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4583
* [DOC] Explaining how Decoder works by man-shu in https://github.com/nilearn/nilearn/pull/4437
* [DOC] Demonstrate how to compute & plot functional connectivity for each hemisphere separately with Yeo 17 networks by victoris93 in https://github.com/nilearn/nilearn/pull/4585
* [STY] fix ruff pandas error by Remi-Gau in https://github.com/nilearn/nilearn/pull/4597
* [FIX] fix error PTH122 from by hndgzkn in https://github.com/nilearn/nilearn/pull/4590
* [STY] fix simplify ruff errors by Remi-Gau in https://github.com/nilearn/nilearn/pull/4599
* [STY] fix numpy ruff error by Remi-Gau in https://github.com/nilearn/nilearn/pull/4598
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4609
* [REF] fix ruff 'errors' by Remi-Gau in https://github.com/nilearn/nilearn/pull/4602
* [REF] fix refactor 'errors' flagged by ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4600
* [REF] fix comprehension 'errors' flagged by ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4601
* [STY] fix fly and up errors flagged by ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4611
* [FIX] fix error PTH106 by hndgzkn in https://github.com/nilearn/nilearn/pull/4607
* [STY] fixes several PERF error flagged by ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4614
* [FIX] fix several errors (PTH112, PTH114, PTH117) by hndgzkn in https://github.com/nilearn/nilearn/pull/4612
* [STY] Fix `PTH118` for all files except in `nilearn.datasets` by michellewang in https://github.com/nilearn/nilearn/pull/4606
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4621
* [STY] fixes simplify error flagged by ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4616
* [FIX] check type compatibility of GLM mask and input data by Remi-Gau in https://github.com/nilearn/nilearn/pull/4603
* [FIX] fix several errors (PTH202, PTH203, PTH204) by hndgzkn in https://github.com/nilearn/nilearn/pull/4618
* [FIX] Fix doc strings for path by Remi-Gau in https://github.com/nilearn/nilearn/pull/4623
* [REF] refactor check matplotlib and plotly by Remi-Gau in https://github.com/nilearn/nilearn/pull/4527
* [ENH] Add `SurfaceImage.from_volume` by jeromedockes in https://github.com/nilearn/nilearn/pull/4593
* [STY] Fix some naming errors flagged by ruff by Remi-Gau in https://github.com/nilearn/nilearn/pull/4624
* [STY] Resolve several PTH issues by PrakharJain1509 in https://github.com/nilearn/nilearn/pull/4620
* [ENH] Allow Decoder to work with surface objects by ymzayek in https://github.com/nilearn/nilearn/pull/4205
* [MAINT] support for python 3.13 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4513
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4632
* Return signals if standardisation was not applied, and change the condition when adding signal mean back for psc method by htwangtw in https://github.com/nilearn/nilearn/pull/4604
* [MAINT] Replace tempfile in tests with proper pytest fixtures by Remi-Gau in https://github.com/nilearn/nilearn/pull/4631
* [STY] Fix ruff errors RUF002-3 and RUF005 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4627
* [ENH] Improve plotting contours for `PlotlySurfaceFigure` objects by adding `add_contours` method by psadil in https://github.com/nilearn/nilearn/pull/3949
* [MAINT] Replace `pytest.warns(DeprecationWarning, match = pattern)` with `pytest.deprecated_call(match = pattern)` by victoris93 in https://github.com/nilearn/nilearn/pull/4637
* Test for screening adjustment by man-shu in https://github.com/nilearn/nilearn/pull/4630
* [ENH] Allow saving SurfaceImage data to Gifti files by Remi-Gau in https://github.com/nilearn/nilearn/pull/4589
* [STY] Fix or silence ARG001-3 error (unused argument) by Remi-Gau in https://github.com/nilearn/nilearn/pull/4641
* [STY] Fix or silence ruff error PD901 - use more meaningful variable name than `df` for pandas dataframe by Remi-Gau in https://github.com/nilearn/nilearn/pull/4646
* [REF] Rename `get_mask_volume` by man-shu in https://github.com/nilearn/nilearn/pull/4640
* [MAINT] remove some unecessary warning filters by Remi-Gau in https://github.com/nilearn/nilearn/pull/4649
* [STY] fix PLR1704 (redefined-argument-from-local) by Remi-Gau in https://github.com/nilearn/nilearn/pull/4644
* [DOC] minor changes to examples for better rendering by Remi-Gau in https://github.com/nilearn/nilearn/pull/4651
* [STY] fix or silence N802 error related to name of functions (only use lower case) by Remi-Gau in https://github.com/nilearn/nilearn/pull/4643
* [STY] fix ruff error PD011 - use `.to_numpy()` instead of `.values` for pandas dataframe by Remi-Gau in https://github.com/nilearn/nilearn/pull/4645
* [MAINT] always run tests in random order by Remi-Gau in https://github.com/nilearn/nilearn/pull/4653
* [DOC] Add missing default values to the docstrings in 'nilearn/glm' - part 1 by anupriyakkumari in https://github.com/nilearn/nilearn/pull/4656
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4667
* [FIX] Fix several errors (PTH100, PTH103, PTH119, PTH120) by hndgzkn in https://github.com/nilearn/nilearn/pull/4648
* [DOC] Add missing default values to the docstrings in 'nilearn/glm' - part 2 by anupriyakkumari in https://github.com/nilearn/nilearn/pull/4659
* [DOC] Add missing default values to the docstrings in 'nilearn/plotting' by anupriyakkumari in https://github.com/nilearn/nilearn/pull/4660
* [FIX] Warn if smoothing_fwhm parameter passed to FLM for surface data by emdupre in https://github.com/nilearn/nilearn/pull/4666
* [MAINT] minor fixes on maintenance scripts by Remi-Gau in https://github.com/nilearn/nilearn/pull/4655
* [STY] fix SIM117 error by Remi-Gau in https://github.com/nilearn/nilearn/pull/4670
* [FIX] Fix several errors (PTH101, PTH102, PTH107, PTH110, PTH111, PTH113, PTH201) in `nilearn.datasets` package by hndgzkn in https://github.com/nilearn/nilearn/pull/4671
* [DOC][MAINT] build doc with minimum version of python and dependencies by Remi-Gau in https://github.com/nilearn/nilearn/pull/4650
* [DOC] use new surface API in plot_surface_bids_analysis by Remi-Gau in https://github.com/nilearn/nilearn/pull/4682
* [DOC] use new surface API in plot_localizer_surface_analysis by Remi-Gau in https://github.com/nilearn/nilearn/pull/4681
* [DOC] use new surface API in plot_surf_stat_map by Remi-Gau in https://github.com/nilearn/nilearn/pull/4683
* [TEST] Clean surface fixtures by man-shu in https://github.com/nilearn/nilearn/pull/4657
* [STY] Fix PTH123 by hndgzkn in https://github.com/nilearn/nilearn/pull/4677
* [MAINT] move surface report tests by Remi-Gau in https://github.com/nilearn/nilearn/pull/4687
* [FIX] Make load_confounds return None for confounds if no cleaning strategy is provided by mibur1 in https://github.com/nilearn/nilearn/pull/4636
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4690
* [FIX] Silence B018 errors by Remi-Gau in https://github.com/nilearn/nilearn/pull/4675
* [MAINT] speed up some tests for first level GLM and interface/bids by Remi-Gau in https://github.com/nilearn/nilearn/pull/4629
* [STY] Fix remaining `PTH118` errors in `nilearn.datasets` by michellewang in https://github.com/nilearn/nilearn/pull/4676
* [MAINT] enact deprecations due for 0.11.0 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4517
* [ENH] add a function to help reporting post-masking atlas in LabelsMaskers by mtorabi59 in https://github.com/nilearn/nilearn/pull/4500
* [DOC] use new surface API in plot_3d_map_to_surface_projection by Remi-Gau in https://github.com/nilearn/nilearn/pull/4674
* [ENH] move experimental surface plotting into the stable API by Remi-Gau in https://github.com/nilearn/nilearn/pull/4688
* [FIX] do not use scaling_axis in example by Remi-Gau in https://github.com/nilearn/nilearn/pull/4694
* [STY] Fix `PTH123` in `nilearn.datasets` by michellewang in https://github.com/nilearn/nilearn/pull/4696
* [MAINT] move surface IO module to stable surface API by Remi-Gau in https://github.com/nilearn/nilearn/pull/4685
* [DOC] use new surface API in plot_surf_atlas by Remi-Gau in https://github.com/nilearn/nilearn/pull/4678
* [MAINT] remove useles test line by Remi-Gau in https://github.com/nilearn/nilearn/pull/4699
* [ENH] Improved SearchLight with NIfTI Support, Mask Handling, and Reusable Transform Method by PrakharJain1509 in https://github.com/nilearn/nilearn/pull/4652
* [REF] Refactor function 'add_graph' in nilearn/plotting/displays/_projectors.py by anupriyakkumari in https://github.com/nilearn/nilearn/pull/4635
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4705
* [DOC] Apply codespell by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4703
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4706
* [FIX] Fix bug in `fetch_single_file` with `resume=True` and improve tests by michellewang in https://github.com/nilearn/nilearn/pull/4701
* Maint/refactor old numpy by hndgzkn in https://github.com/nilearn/nilearn/pull/4689
* [MAINT] check estimators compliance with the scikit-learn recommendations by Remi-Gau in https://github.com/nilearn/nilearn/pull/4547
* [REF] use path for resolve globbing by Remi-Gau in https://github.com/nilearn/nilearn/pull/4658
* [MAINT] remove dependency on matplotlib to filter packages to be tested by hndgzkn in https://github.com/nilearn/nilearn/pull/4709
* [DOC] Surface API explainer by man-shu in https://github.com/nilearn/nilearn/pull/4665
* [DOC] move example for surface API plot_surface_image_and_maskers by Remi-Gau in https://github.com/nilearn/nilearn/pull/4684
* [ENH] Add plotting contours using SurfaceImage with plotly by Remi-Gau in https://github.com/nilearn/nilearn/pull/4713
* [DOC] Use SurfaceImage object for the Searchlight surface example by Remi-Gau in https://github.com/nilearn/nilearn/pull/4711
* [ENH] Handling of SurfaceData in compute_contrast by bthirion in https://github.com/nilearn/nilearn/pull/4610
* [DOC] add link to masking functions by Remi-Gau in https://github.com/nilearn/nilearn/pull/4718
* [FIX] GitHub workflow script injection by joycebrum in https://github.com/nilearn/nilearn/pull/4722
* [STY] Apply assorted ruff rules by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4704
* [MAINT] run tests in parallel by Remi-Gau in https://github.com/nilearn/nilearn/pull/4673
* [ENH] move SurfaceMasker to stable part of the code base by Remi-Gau in https://github.com/nilearn/nilearn/pull/4692
* [DOC] minor RST fixes to improve doc rendering by Remi-Gau in https://github.com/nilearn/nilearn/pull/4726
* [ENH] Move experimental surface classes to the stable API by Remi-Gau in https://github.com/nilearn/nilearn/pull/4723
* [MAINT] fix failure windows with Python 3.9 and matplotlib==3.3.0 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4721
* [MAINT] use pathlib.Path more systematically in nilearn.datasets by Remi-Gau in https://github.com/nilearn/nilearn/pull/4725
* [DOC] update internal references to SurfaceImage classes in doc strings by Remi-Gau in https://github.com/nilearn/nilearn/pull/4727
* [STY] Enforce ruff/flake8-pie rules (PIE) by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4732
* [STY] Enforce ruff/pygrep-hooks rules (PGH) by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4731
* [STY] Apply ruff/flake8-implicit-str-concat rules (ISC) by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4730
* [STY] Enforce ruff/refurb rules (FURB) by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4752
* [MAINT] Expression not assigned by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4751
* [MAINT] String statement has no effect by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4750
* [MAINT] Pythagorean calculation with sub-optimal numerics by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4748
* [STY] Appending to list following its definition by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4747
* [STY] Unnecessary use of `json.loads()` for file data by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4746
* [STY] Simplify chained comparison by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4745
* [MAINT] Exception arguments suggest string formatting by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4744
* [MAINT] Undefined name in `__all__` by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4734
* [STY] Multiple imports for an import name by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4735
* [STY] Comparison with callable by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4737
* [STY] np.testing.assert_ → assert by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4738
* [STY] Unnecessary `None` provided as default by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4741
* [STY] Use of an unneeded `not` by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4742
* Bump codecov/codecov-action from 4 to 5 by dependabot in https://github.com/nilearn/nilearn/pull/4757
* [ENH] move SurfaceLabelMasker to stable API by Remi-Gau in https://github.com/nilearn/nilearn/pull/4714
* [ENH] Allow to run clustering on SurfaceImage by Remi-Gau in https://github.com/nilearn/nilearn/pull/4577
* [ENH] move experimental datasets into stable API by Remi-Gau in https://github.com/nilearn/nilearn/pull/4693
* [ENH] run fit and transform of SurfaceMasker on list of Surface images by Remi-Gau in https://github.com/nilearn/nilearn/pull/4719
* [FIX][DOC] fix doc build by Remi-Gau in https://github.com/nilearn/nilearn/pull/4763
* [FIX] update checks estimators - fix compatibibility issues with scikit-learn >1.5.2 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4724
* [DOC] reorder classes and functions in doc by Remi-Gau in https://github.com/nilearn/nilearn/pull/4766
* Use the estimator type tags as required by scikit-learn 1.6.0 by man-shu in https://github.com/nilearn/nilearn/pull/4774
* [STY] Appending to dictionary following its definition by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4740
* [MAINT] Special method should return `NotImplemented` by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4749
* [FIX] add version added in the new classes and functions by Remi-Gau in https://github.com/nilearn/nilearn/pull/4772
* [STY] Explicit exception raised in the assert message by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4733
* [FIX] Force the parts of PolyData to be 2D by Remi-Gau in https://github.com/nilearn/nilearn/pull/4771
* [MAINT] Sequence value overwritten unconditionally by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4743
* [ENH] Allow SurfaceLabelsMasker to work with a list of Surface images by man-shu in https://github.com/nilearn/nilearn/pull/4770
* [MAINT] Disable ruff rules conflicting with the formatter by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4753
* [MAINT] Apply repo-review rules by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4754
* [MAINT] Make sure only changed examples are rebuilt on PR by Remi-Gau in https://github.com/nilearn/nilearn/pull/4780
* Module imports itself by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4778
* [DOC] fix doc string to remove warning in doc build by Remi-Gau in https://github.com/nilearn/nilearn/pull/4782
* [DOC] split atlases section by probabilistic and deterministic by Remi-Gau in https://github.com/nilearn/nilearn/pull/4779
* [STY] Implicit enumerate calls by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4785
* [DOC] fix rendering hrf list by Remi-Gau in https://github.com/nilearn/nilearn/pull/4784
* [MAINT] Update ruff to 0.8.0 by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4786
* [DOC] improve doc regarding events with 0 duration by Remi-Gau in https://github.com/nilearn/nilearn/pull/4776
* [FIX] create parent doc for `.nojekyll` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4788
* [MAINT] allow possiblity to skip doc build or test in CI via specific commit message by Remi-Gau in https://github.com/nilearn/nilearn/pull/4783
* [DOC] Fix rendering of attributes by Remi-Gau in https://github.com/nilearn/nilearn/pull/4787
* [ENH] make the number of vertices the first dimension of image data by jeromedockes in https://github.com/nilearn/nilearn/pull/4591
* [DOC] Fix render of lists, notes and code blocks in 'template' parameters by Remi-Gau in https://github.com/nilearn/nilearn/pull/4790
* [ENH] run GLM on surface data on BIDS datasets by Remi-Gau in https://github.com/nilearn/nilearn/pull/4507
* [MAINT] increase coverage by Remi-Gau in https://github.com/nilearn/nilearn/pull/4794
* [STY] Use `.items()` to iterate over the dictionary by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4798
* [MAINT] update checks scikit learn >= 1.7 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4796
* [DOC] move doc string for classes out of constructor by Remi-Gau in https://github.com/nilearn/nilearn/pull/4795
* [STY] Implicit enumerate calls by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4799
* [DOC] add bluesky to footer by Remi-Gau in https://github.com/nilearn/nilearn/pull/4800
* [FIX] allow t_r, high_pass, low_pass to be int in signal.clean by Remi-Gau in https://github.com/nilearn/nilearn/pull/4804
* [FIX] Allow single 4D nifti as input for SecondLevelModel by Remi-Gau in https://github.com/nilearn/nilearn/pull/4806
* [STY] Unused import by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4812
* [ENH] Remove old surface by man-shu in https://github.com/nilearn/nilearn/pull/4791
* [ENH] revert coercing surface data to 2D by Remi-Gau in https://github.com/nilearn/nilearn/pull/4793
* [ENH] allow to ignore certain BIDS entities when using query_bids by Remi-Gau in https://github.com/nilearn/nilearn/pull/4802
* [DOC][FIX] update number of participants loaded in load_nki by Remi-Gau in https://github.com/nilearn/nilearn/pull/4817
* [ENH] fit second level model on surface by Remi-Gau in https://github.com/nilearn/nilearn/pull/4715
* [REL] 0.11.0 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4813
* [FIX] rework plot_surf_atlas example by Remi-Gau in https://github.com/nilearn/nilearn/pull/4836
* [FIX] update plot_surface_bids_analysis by Remi-Gau in https://github.com/nilearn/nilearn/pull/4841
* [FIX] update plot_3d_map_to_surface_projection by Remi-Gau in https://github.com/nilearn/nilearn/pull/4837
* [FIX] update plot_surf_stat_map to properly use surface api by Remi-Gau in https://github.com/nilearn/nilearn/pull/4838
* [FIX] update plot_surface_101 example by Remi-Gau in https://github.com/nilearn/nilearn/pull/4834
* [FIX] update plot_surface_image_and_maskers.py by Remi-Gau in https://github.com/nilearn/nilearn/pull/4835
* [FIX] update plot_localizer_surface_analysis by Remi-Gau in https://github.com/nilearn/nilearn/pull/4840

New Contributors
* alexsayal made their first contribution in https://github.com/nilearn/nilearn/pull/4416
* YCHuang0610 made their first contribution in https://github.com/nilearn/nilearn/pull/4407
* ajoshiusc made their first contribution in https://github.com/nilearn/nilearn/pull/4412
* arovai made their first contribution in https://github.com/nilearn/nilearn/pull/4483
* muddi900 made their first contribution in https://github.com/nilearn/nilearn/pull/4476
* victoris93 made their first contribution in https://github.com/nilearn/nilearn/pull/4558
* kaitj made their first contribution in https://github.com/nilearn/nilearn/pull/4571
* tharun634 made their first contribution in https://github.com/nilearn/nilearn/pull/4582
* hndgzkn made their first contribution in https://github.com/nilearn/nilearn/pull/4590
* PrakharJain1509 made their first contribution in https://github.com/nilearn/nilearn/pull/4620
* anupriyakkumari made their first contribution in https://github.com/nilearn/nilearn/pull/4656
* mibur1 made their first contribution in https://github.com/nilearn/nilearn/pull/4636
* joycebrum made their first contribution in https://github.com/nilearn/nilearn/pull/4722

**Full Changelog**: https://github.com/nilearn/nilearn/compare/0.10.4...0.11.0